October 2009 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2898: Changes to User Menu and History|Options menu....
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2e593cbb6c69 changeset: 2898:2e593cbb6c69 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Oct 20 18:00:08 2009 -0400 description: Changes to User Menu and History|Options menu. User menu now provides direct links to user's histories and datasets. History|Options menu no longer uses the adjective 'My.' 2 file(s) affected in this change: templates/base_panels.mako templates/root/index.mako diffs (46 lines): diff -r ed8ea4318e9a -r 2e593cbb6c69 templates/base_panels.mako --- a/templates/base_panels.mako Tue Oct 20 16:53:18 2009 -0400 +++ b/templates/base_panels.mako Tue Oct 20 18:00:08 2009 -0400 @@ -217,13 +217,12 @@ %endif </ul> <ul class="loggedin-only" style="${style2}"> - <li>Logged in as <span id="user-email">${user_email}</span></li> - <li><a target="galaxy_main" href="${h.url_for( controller='root', action='my_data' )}">My Data</a></li> %if app.config.use_remote_user: %if app.config.remote_user_logout_href: <li><a href="${app.config.remote_user_logout_href}" target="_top">Logout</a></li> %endif %else: + <li>Logged in as <span id="user-email">${user_email}</span></li> <li><a target="galaxy_main" href="${h.url_for( controller='user', action='index' )}">Preferences</a></li> <% if app.config.require_login: @@ -233,7 +232,10 @@ logout_target = "galaxy_main" logout_url = h.url_for( controller='user', action='logout' ) %> - <li><a target="${logout_target}" href="${logout_url}">Logout</a></li> + <li><a target="${logout_target}" href="${logout_url}">Logout ${user_email}</a></li> + <li><hr style="color: inherit; background-color: gray"/></li> + <li><a target="galaxy_main" href="${h.url_for( controller='history', action='list' )}">Histories</a></li> + <li><a target="galaxy_main" href="${h.url_for( controller='dataset', action='list' )}">Datasets</a></li> %endif </ul> </div> diff -r ed8ea4318e9a -r 2e593cbb6c69 templates/root/index.mako --- a/templates/root/index.mako Tue Oct 20 16:53:18 2009 -0400 +++ b/templates/root/index.mako Tue Oct 20 18:00:08 2009 -0400 @@ -7,10 +7,10 @@ $("#history-options-button").css( "position", "relative" ); make_popupmenu( $("#history-options-button"), { "History Lists": null, - "My Saved Histories": function() { + "Saved Histories": function() { galaxy_main.location = "${h.url_for( controller='history', action='list')}"; }, - "My Shared Histories": function() { + "Shared Histories": function() { galaxy_main.location = "${h.url_for( controller='history', action='list', operation='sharing' )}"; }, "Histories Shared with Me": function() {

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[hg] galaxy 2899: Remove debugging stmt.
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4252c14c0063 changeset: 2899:4252c14c0063 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Wed Oct 21 10:21:48 2009 -0400 description: Remove debugging stmt. 1 file(s) affected in this change: templates/base_panels.mako diffs (12 lines): diff -r 2e593cbb6c69 -r 4252c14c0063 templates/base_panels.mako --- a/templates/base_panels.mako Tue Oct 20 18:00:08 2009 -0400 +++ b/templates/base_panels.mako Wed Oct 21 10:21:48 2009 -0400 @@ -232,7 +232,7 @@ logout_target = "galaxy_main" logout_url = h.url_for( controller='user', action='logout' ) %> - <li><a target="${logout_target}" href="${logout_url}">Logout ${user_email}</a></li> + <li><a target="${logout_target}" href="${logout_url}">Logout</a></li> <li><hr style="color: inherit; background-color: gray"/></li> <li><a target="galaxy_main" href="${h.url_for( controller='history', action='list' )}">Histories</a></li> <li><a target="galaxy_main" href="${h.url_for( controller='dataset', action='list' )}">Datasets</a></li>

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[hg] galaxy 2901: revert root.py (backward compatibility issue)
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2950f021fc0c changeset: 2901:2950f021fc0c user: Kanwei Li <kanwei(a)gmail.com> date: Wed Oct 21 14:16:38 2009 -0400 description: revert root.py (backward compatibility issue) 1 file(s) affected in this change: lib/galaxy/web/controllers/root.py diffs (58 lines): diff -r 197ff8461127 -r 2950f021fc0c lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Wed Oct 21 11:53:29 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Wed Oct 21 14:16:38 2009 -0400 @@ -139,13 +139,49 @@ @web.expose def display( self, trans, id=None, hid=None, tofile=None, toext=".txt", **kwd ): """ - Backward compatibility. + Returns data directly into the browser. + Sets the mime-type according to the extension """ - if tofile: - to_ext = toext + if hid is not None: + try: + hid = int( hid ) + except: + return "hid '%s' is invalid" %str( hid ) + history = trans.get_history() + for dataset in history.datasets: + if dataset.hid == hid: + data = dataset + break + else: + raise Exception( "No dataset with hid '%d'" % hid ) else: - to_ext = None - return trans.webapp.controllers['dataset'].display( trans, encoded_id=id, to_ext=to_ext ) + try: + data = self.app.model.HistoryDatasetAssociation.get( id ) + except: + return "Dataset id '%s' is invalid" %str( id ) + if data: + user, roles = trans.get_user_and_roles() + if trans.app.security_agent.can_access_dataset( roles, data.dataset ): + mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) + trans.response.set_content_type(mime) + if tofile: + fStat = os.stat(data.file_name) + trans.response.headers['Content-Length'] = int(fStat.st_size) + if toext[0:1] != ".": + toext = "." + toext + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = data.name + fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] + trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (data.hid, fname, toext) + trans.log_event( "Display dataset id: %s" % str(id) ) + try: + return open( data.file_name ) + except: + return "This dataset contains no content" + else: + return "You are not allowed to access this dataset" + else: + return "No dataset with id '%s'" % str( id ) @web.expose def display_child(self, trans, parent_id=None, designation=None, tofile=None, toext=".txt"):

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[hg] galaxy 2900: Make HDA grid unicode compatible.
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/197ff8461127 changeset: 2900:197ff8461127 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Wed Oct 21 11:53:29 2009 -0400 description: Make HDA grid unicode compatible. 1 file(s) affected in this change: templates/dataset/grid.mako diffs (12 lines): diff -r 4252c14c0063 -r 197ff8461127 templates/dataset/grid.mako --- a/templates/dataset/grid.mako Wed Oct 21 10:21:48 2009 -0400 +++ b/templates/dataset/grid.mako Wed Oct 21 11:53:29 2009 -0400 @@ -260,6 +260,8 @@ %> %for cellnum, v in enumerate( value ): <% + if isinstance(v, str): + v = unicode(v, 'utf-8') # Attach popup menu? if column.attach_popup and cellnum == 0: extra = '<a id="grid-%d-popup" class="arrow" style="display: none;"><span>▼</span></a>' % i

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[hg] galaxy 2902: Style updates to external view of history.
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2f3c4dd6ff1a changeset: 2902:2f3c4dd6ff1a user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Wed Oct 21 14:19:45 2009 -0400 description: Style updates to external view of history. 3 file(s) affected in this change: static/june_2007_style/autocomplete_tagging.css.tmpl static/june_2007_style/blue/autocomplete_tagging.css templates/history/view.mako diffs (211 lines): diff -r 2950f021fc0c -r 2f3c4dd6ff1a static/june_2007_style/autocomplete_tagging.css.tmpl --- a/static/june_2007_style/autocomplete_tagging.css.tmpl Wed Oct 21 14:16:38 2009 -0400 +++ b/static/june_2007_style/autocomplete_tagging.css.tmpl Wed Oct 21 14:19:45 2009 -0400 @@ -129,5 +129,5 @@ .delete-tag-img { - margin-left: 0.3em + margin-left: 0.3em; } \ No newline at end of file diff -r 2950f021fc0c -r 2f3c4dd6ff1a static/june_2007_style/blue/autocomplete_tagging.css --- a/static/june_2007_style/blue/autocomplete_tagging.css Wed Oct 21 14:16:38 2009 -0400 +++ b/static/june_2007_style/blue/autocomplete_tagging.css Wed Oct 21 14:19:45 2009 -0400 @@ -1,133 +1,18 @@ -/****************************************************************************/ -/* JQuery autocomplete code */ -/****************************************************************************/ - -.ac_results { - padding: 0px; - border: 1px solid black; - background-color: white; - overflow: hidden; - z-index: 99999; -} - -.ac_results ul { - width: 100%; - list-style-position: outside; - list-style: none; - padding: 0; - margin: 0; -} - -.ac_results li { - padding: 2px 5px; - cursor: default; - display: block; - /* - if width will be 100% horizontal scrollbar will apear - when scroll mode will be used - */ - /*width: 100%;*/ - /* font: menu; */ - font-size: 12px; - /* - it is very important, if line-height not setted or setted - in relative units scroll will be broken in firefox - */ - line-height: 16px; - overflow: hidden; -} - -.ac_loading { - background: white url('indicator.gif') right center no-repeat; -} - -.ac_odd { - background-color: #fff; /* #eee */ - margin-left: 0.3em; -} - -.ac_even { - margin-left: 0.3em; -} - -.ac_over { - background-color: #0A246A; - color: white; -} - -.ac_header { - font-style: normal; - color: gray; - border-bottom: 0.1em solid gray; -} - -/****************************************************************************/ -/* Custom code for supporting tags */ -/****************************************************************************/ -.tag-area { - width: 100%; - cursor: pointer; - border: solid 1px #eee; -} - -.active-tag-area { - background-color: white; -} - -.toggle-link -{ - font-weight: normal; - padding: 0.3em; - margin-bottom: 1em; - width: 100%; - padding: 0.2em 0em 0.2em 0em; -} - -.tag-button { - width: auto; - color: #444; - text-decoration: none; - display: inline-block; - cursor: pointer; - margin: 0.2em; - border: 0; - padding: 0.1em 0.5em 0.1em 0.5em; - -moz-border-radius: .5em; - -webkit-border-radius: .5em; - border-radius: .5em; - background:#bbb; -} - -.tag-button img -{ - padding-left: 0.4em; -} - -.tag-button .tag-name:hover -{ - color: white; -} - -.add-tag-button -{ - margin-bottom: 0.3em; - vertical-align: middle; - padding: 0.3em; -} - -.add-tag-button:hover -{ - cursor: pointer; -} - -.tag-input { - vertical-align: bottom; - border: none; - outline: none; -} - -.delete-tag-img -{ - - margin-left: 0.3em -} \ No newline at end of file +.ac_results{padding:0px;border:1px solid black;background-color:white;overflow:hidden;z-index:99999;} +.ac_results ul{width:100%;list-style-position:outside;list-style:none;padding:0;margin:0;} +.ac_results li{padding:2px 5px;cursor:default;display:block;font-size:12px;line-height:16px;overflow:hidden;} +.ac_loading{background:white url('indicator.gif') right center no-repeat;} +.ac_odd{background-color:#fff;margin-left:0.3em;} +.ac_even{margin-left:0.3em;} +.ac_over{background-color:#0A246A;color:white;} +.ac_header{font-style:normal;color:gray;border-bottom:0.1em solid gray;} +.tag-area{width:100%;cursor:pointer;border:solid 1px #eee;} +.active-tag-area{background-color:white;} +.toggle-link{font-weight:normal;padding:0.3em;margin-bottom:1em;width:100%;padding:0.2em 0em 0.2em 0em;} +.tag-button{width:auto;color:#444;text-decoration:none;display:inline-block;cursor:pointer;margin:0.2em;border:0;padding:0.1em 0.5em 0.1em 0.5em;-moz-border-radius:.5em;-webkit-border-radius:.5em;border-radius:.5em;background:#bbb;} +.tag-button img{padding-left:0.4em;} +.tag-button .tag-name:hover{color:white;} +.add-tag-button{margin-bottom:0.3em;vertical-align:middle;padding:0.3em;} +.add-tag-button:hover{cursor:pointer;} +.tag-input{vertical-align:bottom;border:none;outline:none;} +.delete-tag-img{margin-left:0.3em;} diff -r 2950f021fc0c -r 2f3c4dd6ff1a templates/history/view.mako --- a/templates/history/view.mako Wed Oct 21 14:16:38 2009 -0400 +++ b/templates/history/view.mako Wed Oct 21 14:19:45 2009 -0400 @@ -8,6 +8,13 @@ <%def name="stylesheets()"> ${parent.stylesheets()} ${h.css( "history", "autocomplete_tagging" )} + <style type="text/css"> + .visible-right-border { + padding-right: 3px; + border-right-style: solid; + border-right-color: #66AA66; + }; + </style> </%def> <%namespace file="/root/history_common.mako" import="render_dataset" /> @@ -291,7 +298,7 @@ <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> %if not user_owns_history: - <a href="${h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id) )}">${_('import')}</a> | + <a href="${h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id) )}">import and start using history</a> | %endif <a href="${h.url_for( controller='history', action='view', id=trans.security.encode_id(history.id) )}">${_('refresh')}</a> %if show_deleted: @@ -320,7 +327,7 @@ %if trans.get_user() is not None: <div id='history-tag-area' class="tag-element"></div> - ${render_tagging_element(history, "history-tag-area", get_toggle_link_text_fn='get_toggle_link_text', editable=user_owns_history)} + ${render_tagging_element(history, "history-tag-area", use_toggle_link='false', get_toggle_link_text_fn='get_toggle_link_text', editable=user_owns_history)} %endif %if not datasets: @@ -332,7 +339,7 @@ ## Render requested datasets, ordered from newest to oldest %for data in reversed( datasets ): %if data.visible: - <div class="historyItemContainer" id="historyItemContainer-${data.id}"> + <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, user_owns_dataset=user_owns_history )} </div> %endif

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[hg] galaxy 2903: New functional test harness. Update to recent ...
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/fd5943ff7b40 changeset: 2903:fd5943ff7b40 user: James Taylor <james(a)jamestaylor.org> date: Tue Oct 20 13:08:29 2009 -0400 description: New functional test harness. Update to recent nose. No longer rely on nose to manage the embedded web server (this is not done in functional_tests.py). Log page contents to a temporary file on check_page_for_string error. [mq]: functional-test-harness 7 file(s) affected in this change: eggs.ini lib/galaxy/eggs/__init__.py lib/galaxy/model/migrate/check.py run_functional_tests.sh scripts/functional_tests.py test/base/twilltestcase.py test/functional/__init__.py diffs (585 lines): diff -r 2f3c4dd6ff1a -r fd5943ff7b40 eggs.ini --- a/eggs.ini Wed Oct 21 14:19:45 2009 -0400 +++ b/eggs.ini Tue Oct 20 13:08:29 2009 -0400 @@ -34,8 +34,8 @@ ;lsprof - james Mako = 0.2.5 MyghtyUtils = 0.52 -nose = 0.9.1 -NoseHTML = 0.2 +nose = 0.11.1 +NoseHTML = 0.3 Paste = 1.5.1 PasteDeploy = 1.3.1 PasteScript = 1.3.6 @@ -60,7 +60,7 @@ python_lzo = _static flup = .dev_r2311 bx_python = _dev_r4bf1f32e6b76 -nose = .dev_r101 +; nose = .dev_r7156749efc58 ; source location, necessary for scrambling [source] @@ -82,8 +82,8 @@ lrucache = http://evan.prodromou.name/lrucache/lrucache-0.2.tar.gz Mako = http://www.makotemplates.org/downloads/Mako-0.2.5.tar.gz MyghtyUtils = http://cheeseshop.python.org/packages/source/M/MyghtyUtils/MyghtyUtils-0.52… -nose = http://www.somethingaboutorange.com/mrl/projects/nose/nose-0.9.1.tar.gz -NoseHTML = http://dist.g2.bx.psu.edu/nosehtml-0.2.tar.bz2 +nose = http://pypi.python.org/packages/source/n/nose/nose-0.11.1.tar.gz +NoseHTML = http://bitbucket.org/james_taylor/nosehtml/get/c46a54d569ae.bz2 Paste = http://cheeseshop.python.org/packages/source/P/Paste/Paste-1.5.1.tar.gz PasteDeploy = http://cheeseshop.python.org/packages/source/P/PasteDeploy/PasteDeploy-1.3.… PasteScript = http://cheeseshop.python.org/packages/source/P/PasteScript/PasteScript-1.3.… diff -r 2f3c4dd6ff1a -r fd5943ff7b40 lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py Wed Oct 21 14:19:45 2009 -0400 +++ b/lib/galaxy/eggs/__init__.py Tue Oct 20 13:08:29 2009 -0400 @@ -2,7 +2,7 @@ Manage Galaxy eggs """ -import os, sys, shutil, tarfile, zipfile, subprocess, ConfigParser, glob, urllib2 +import os, sys, shutil, tarfile, zipfile, zipimport, subprocess, ConfigParser, glob, urllib2, shutil from types import ModuleType import logging @@ -101,10 +101,17 @@ raise EggNotFetchable( self.name ) #if e.code == 404: # return False + self.unpack_if_needed() for doppelganger in self.doppelgangers: - os.unlink( doppelganger ) + remove_file_or_path( doppelganger ) log.debug( "Removed conflicting egg: %s" % doppelganger ) return True + def unpack_if_needed( self ): + meta = pkg_resources.EggMetadata( zipimport.zipimporter( self.path ) ) + if meta.has_metadata( 'not-zip-safe' ): + unpack_zipfile( self.path, self.path + "-tmp" ) + os.remove( self.path ) + os.rename( self.path + "-tmp", self.path ) def scramble( self ): if self.path is None: self.find() @@ -141,8 +148,9 @@ shutil.copyfile( new_egg, self.path ) log.warning( "scramble(): Copied egg to:" ) log.warning( " %s" % self.path ) + self.unpack_if_needed() for doppelganger in self.doppelgangers: - os.unlink( doppelganger ) + remove_file_or_path( doppelganger ) log.warning( "Removed conflicting egg: %s" % doppelganger ) return True # scramble helper methods @@ -584,4 +592,37 @@ else: return "%s-noplatform" % get_py() +def unpack_zipfile( filename, extract_dir): + z = zipfile.ZipFile(filename) + try: + for info in z.infolist(): + name = info.filename + # don't extract absolute paths or ones with .. in them + if name.startswith('/') or '..' in name: + continue + target = os.path.join(extract_dir, *name.split('/')) + if not target: + continue + if name.endswith('/'): + # directory + pkg_resources.ensure_directory(target) + else: + # file + pkg_resources.ensure_directory(target) + data = z.read(info.filename) + f = open(target,'wb') + try: + f.write(data) + finally: + f.close() + del data + finally: + z.close() + +def remove_file_or_path( f ): + if os.path.isdir( f ): + shutil.rmtree( f ) + else: + os.remove( f ) + pkg_resources.require = require diff -r 2f3c4dd6ff1a -r fd5943ff7b40 lib/galaxy/model/migrate/check.py --- a/lib/galaxy/model/migrate/check.py Wed Oct 21 14:19:45 2009 -0400 +++ b/lib/galaxy/model/migrate/check.py Tue Oct 20 13:08:29 2009 -0400 @@ -1,4 +1,4 @@ -import os.path, logging +import sys, os.path, logging from galaxy import eggs @@ -109,4 +109,18 @@ for ver, change in changeset: nextver = ver + changeset.step log.info( 'Migrating %s -> %s... ' % ( ver, nextver ) ) - schema.runchange( ver, change, changeset.step ) + old_stdout = sys.stdout + class FakeStdout( object ): + def __init__( self ): + self.buffer = [] + def write( self, s ): + self.buffer.append( s ) + def flush( self ): + pass + sys.stdout = FakeStdout() + try: + schema.runchange( ver, change, changeset.step ) + finally: + for message in "".join( sys.stdout.buffer ).split( "\n" ): + log.info( message ) + sys.stdout = old_stdout \ No newline at end of file diff -r 2f3c4dd6ff1a -r fd5943ff7b40 run_functional_tests.sh --- a/run_functional_tests.sh Wed Oct 21 14:19:45 2009 -0400 +++ b/run_functional_tests.sh Tue Oct 20 13:08:29 2009 -0400 @@ -5,7 +5,7 @@ rm -f run_functional_tests.log if [ ! $1 ]; then - python -ES ./scripts/nosetests.py -v -w test --with-nosehtml --html-report-file run_functional_tests.html --exclude="^get" functional + python -ES ./scripts/functional_tests.py -v --with-nosehtml --html-report-file run_functional_tests.html --exclude="^get" functional elif [ $1 = 'help' ]; then echo "'run_functional_tests.sh' for testing all the tools in functional directory" echo "'run_functional_tests.sh aaa' for testing one test case of 'aaa' ('aaa' is the file name with path)" @@ -13,16 +13,16 @@ echo "'run_functional_tests.sh -sid ccc' for testing one section with sid 'ccc' ('ccc' is the string after 'section::')" echo "'run_functional_tests.sh -list' for listing all the tool ids" elif [ $1 = '-id' ]; then - python -ES ./scripts/nosetests.py -v -w test functional.test_toolbox:TestForTool_$2 --with-nosehtml --html-report-file run_functional_tests.html + python -ES ./scripts/functional_tests.py -v functional.test_toolbox:TestForTool_$2 --with-nosehtml --html-report-file run_functional_tests.html elif [ $1 = '-sid' ]; then - python -ES ./scripts/nosetests.py --with-nosehtml --html-report-file run_functional_tests.html -v -w test `python tool_list.py $2` + python -ES ./scripts/functional_tests.py --with-nosehtml --html-report-file run_functional_tests.html -v `python tool_list.py $2` elif [ $1 = '-list' ]; then python tool_list.py echo "===========================================================================================================================================" echo "'run_functional_tests.sh -id bbb' for testing one tool with id 'bbb' ('bbb' is the tool id)" echo "'run_functional_tests.sh -sid ccc' for testing one section with sid 'ccc' ('ccc' is the string after 'section::')" else - python -ES ./scripts/nosetests.py -v -w test --with-nosehtml --html-report-file run_functional_tests.html $1 + python -ES ./scripts/functional_tests.py -v --with-nosehtml --html-report-file run_functional_tests.html $1 fi echo "'run_functional_tests.sh help' for help" diff -r 2f3c4dd6ff1a -r fd5943ff7b40 scripts/functional_tests.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/functional_tests.py Tue Oct 20 13:08:29 2009 -0400 @@ -0,0 +1,211 @@ +#!/usr/bin/env python + +import os, sys + +# Assume we are run from the galaxy root directory, add lib to the python path +cwd = os.getcwd() +new_path = [ os.path.join( cwd, "lib" ) ] +new_path.extend( sys.path[1:] ) +sys.path = new_path + +from galaxy import eggs + +eggs.require( "nose" ) +eggs.require( "NoseHTML" ) +eggs.require( "twill==0.9" ) +eggs.require( "Paste" ) +eggs.require( "PasteDeploy" ) +eggs.require( "Cheetah" ) + +import atexit, logging, os, sys, tempfile +import twill, unittest, time +import os, os.path, subprocess, sys, threading +import httplib +from paste import httpserver +import galaxy.app +from galaxy.app import UniverseApplication +from galaxy.web import buildapp +from galaxy import tools +from galaxy.util import bunch + +log = logging.getLogger( "functional_tests.py" ) + +default_galaxy_test_host = "localhost" +default_galaxy_test_port = "8777" +default_galaxy_locales = 'en' +default_galaxy_test_file_dir = "test-data" + +def main(): + + # ---- Configuration ------------------------------------------------------ + + galaxy_test_host = os.environ.get( 'GALAXY_TEST_HOST', default_galaxy_test_host ) + galaxy_test_port = os.environ.get( 'GALAXY_TEST_PORT', default_galaxy_test_port ) + if 'HTTP_ACCEPT_LANGUAGE' not in os.environ: + os.environ['HTTP_ACCEPT_LANGUAGE'] = default_galaxy_locales + galaxy_test_file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR', default_galaxy_test_file_dir ) + if not os.path.isabs( galaxy_test_file_dir ): + galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir ) + start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ + if start_server: + if 'GALAXY_TEST_DBPATH' in os.environ: + db_path = os.environ['GALAXY_TEST_DBPATH'] + else: + tempdir = tempfile.mkdtemp() + db_path = os.path.join( tempdir, 'database' ) + file_path = os.path.join( db_path, 'files' ) + try: + os.makedirs( file_path ) + except OSError: + pass + if 'GALAXY_TEST_DBURI' in os.environ: + database_connection = os.environ['GALAXY_TEST_DBURI'] + else: + database_connection = 'sqlite:///' + os.path.join( db_path, 'universe.sqlite' ) + if 'GALAXY_TEST_RUNNERS' in os.environ: + start_job_runners = os.environ['GALAXY_TEST_RUNNERS'] + else: + start_job_runners = None + if 'GALAXY_TEST_DEF_RUNNER' in os.environ: + default_cluster_job_runner = os.environ['GALAXY_TEST_DEF_RUNNER'] + else: + default_cluster_job_runner = 'local:///' + + print "Database connection:", database_connection + + # What requires these? + os.environ['GALAXY_TEST_HOST'] = galaxy_test_host + os.environ['GALAXY_TEST_PORT'] = galaxy_test_port + os.environ['GALAXY_TEST_FILE_DIR'] = galaxy_test_file_dir + + # ---- Build Application -------------------------------------------------- + + app = None + + if start_server: + + # Build the Universe Application + app = UniverseApplication( job_queue_workers = 5, + start_job_runners = start_job_runners, + default_cluster_job_runner = default_cluster_job_runner, + id_secret = 'changethisinproductiontoo', + template_path = "templates", + database_connection = database_connection, + file_path = file_path, + tool_config_file = "tool_conf.xml.sample", + datatype_converters_config_file = "datatype_converters_conf.xml.sample", + tool_path = "tools", + tool_parse_help = False, + test_conf = "test.conf", + log_destination = "stdout", + use_heartbeat = False, + allow_user_creation = True, + allow_user_deletion = True, + admin_users = 'test(a)bx.psu.edu', + library_import_dir = galaxy_test_file_dir, + user_library_import_dir = os.path.join( galaxy_test_file_dir, 'users' ), + global_conf = { "__file__": "universe_wsgi.ini.sample" } ) + + log.info( "Embedded Universe application started" ); + + # ---- Run webserver ------------------------------------------------------ + + server = None + + if start_server: + + webapp = buildapp.app_factory( dict(), use_translogger = False, app=app ) + server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) + t = threading.Thread( target=server.serve_forever ) + t.start() + + # Test if the server is up + for i in range( 10 ): + conn = httplib.HTTPConnection( galaxy_test_host, galaxy_test_port ) + conn.request( "GET", "/" ) + if conn.getresponse().status == 200: + break + time.sleep( 0.1 ) + else: + raise Exception( "Test HTTP server did not return '200 OK' after 10 tries" ) + + log.info( "Embedded web server started" ) + + + # ---- Load toolbox for generated tests ----------------------------------- + + # We don't add the tests to the path until everything is up and running + new_path = [ os.path.join( cwd, "test" ) ] + new_path.extend( sys.path[1:] ) + sys.path = new_path + + import functional.test_toolbox + + if app: + # TODO: provisions for loading toolbox from file when using external server + functional.test_toolbox.toolbox = app.toolbox + else: + # FIXME: This doesn't work at all now that toolbox requires an 'app' instance + # (to get at datatypes, might just pass a datatype registry directly) + my_app = bunch.Bunch( datatypes_registry = galaxy.datatypes.registry.Registry() ) + test_toolbox.toolbox = tools.ToolBox( 'tool_conf.xml.test', 'tools', my_app ) + + # ---- Find tests --------------------------------------------------------- + + log.info( "Functional tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_port ) ) + + rval = False + + try: + + import nose.core + import nose.config + import nose.loader + import nose.plugins.manager + + test_config = nose.config.Config( env = os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) + test_config.configure( sys.argv ) + + loader = nose.loader.TestLoader( config = test_config ) + + plug_loader = test_config.plugins.prepareTestLoader( loader ) + if plug_loader is not None: + loader = plug_loader + + tests = loader.loadTestsFromNames( test_config.testNames ) + + test_runner = nose.core.TextTestRunner( + stream = test_config.stream, + verbosity = test_config.verbosity, + config = test_config) + + plug_runner = test_config.plugins.prepareTestRunner( test_runner ) + if plug_runner is not None: + test_runner = plug_runner + + result = test_runner.run( tests ) + + rval = result.wasSuccessful() + + except: + log.exception( "Failure running tests" ) + + log.info( "Shutting down" ) + + # ---- Teardown ----------------------------------------------------------- + + if server: + log.info( "Shutting down embedded web server" ) + server.server_close() + server = None + log.info( "Embedded web server stopped" ) + if app: + log.info( "Shutting down app" ) + app.shutdown() + app = None + log.info( "Embedded Universe application stopped" ) + + return rval + +if __name__ == "__main__": + main() diff -r 2f3c4dd6ff1a -r fd5943ff7b40 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Oct 21 14:19:45 2009 -0400 +++ b/test/base/twilltestcase.py Tue Oct 20 13:08:29 2009 -0400 @@ -1,7 +1,7 @@ import pkg_resources pkg_resources.require( "twill==0.9" ) -import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile +import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile, tempfile from itertools import * import twill @@ -650,14 +650,24 @@ self.visit_page( "user/logout" ) self.check_page_for_string( "You are no longer logged in" ) self.home() + # Functions associated with browsers, cookies, HTML forms and page visits + def check_page_for_string( self, patt ): """Looks for 'patt' in the current browser page""" page = self.last_page() for subpatt in patt.split(): if page.find( patt ) == -1: - errmsg = "TwillAssertionError: no match to '%s'" %patt + fname = self.write_temp_file( page ) + errmsg = "no match to '%s'\npage content written to '%s'" % ( patt, fname ) raise AssertionError( errmsg ) + + def write_temp_file( self, content ): + fd, fname = tempfile.mkstemp( suffix='.html', prefix='twilltestcase-' ) + f = os.fdopen( fd, "w" ) + f.write( content ) + f.close() + return fname def clear_cookies( self ): tc.clear_cookies() @@ -825,7 +835,7 @@ def wait( self, maxiter=20 ): """Waits for the tools to finish""" count = 0 - sleep_amount = 1 + sleep_amount = 0.1 self.home() while count < maxiter: count += 1 @@ -833,7 +843,7 @@ page = tc.browser.get_html() if page.find( '' ) > -1: time.sleep( sleep_amount ) - sleep_amount += 1 + sleep_amount *= 2 else: break self.assertNotEqual(count, maxiter) diff -r 2f3c4dd6ff1a -r fd5943ff7b40 test/functional/__init__.py --- a/test/functional/__init__.py Wed Oct 21 14:19:45 2009 -0400 +++ b/test/functional/__init__.py Tue Oct 20 13:08:29 2009 -0400 @@ -1,131 +1,3 @@ -import atexit, logging, os, sys, tempfile - -import pkg_resources - -pkg_resources.require( "twill==0.9" ) -pkg_resources.require( "Paste" ) -pkg_resources.require( "PasteDeploy" ) -pkg_resources.require( "Cheetah" ) - -import twill, unittest, time -import os, os.path, subprocess, sys, threading -import httplib -from paste import httpserver -import galaxy.app -from galaxy.app import UniverseApplication -from galaxy.web import buildapp -import test_toolbox -from galaxy import tools -from galaxy.util import bunch - -log = logging.getLogger( __name__ ) - -# TODO: should be able to override these, as well as prevent starting th -# server (for running the tests against a running instance) - -default_galaxy_test_host = "localhost" -default_galaxy_test_port = "8777" -default_galaxy_locales = 'en' -galaxy_test_file_dir = "test-data" -server = None -app = None - -def setup(): - """Start the web server for the tests""" - global server, app - - galaxy_test_host = os.environ.get( 'GALAXY_TEST_HOST', default_galaxy_test_host ) - galaxy_test_port = os.environ.get( 'GALAXY_TEST_PORT', default_galaxy_test_port ) - if 'HTTP_ACCEPT_LANGUAGE' not in os.environ: - os.environ['HTTP_ACCEPT_LANGUAGE'] = default_galaxy_locales - - start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ - if start_server: - if 'GALAXY_TEST_DBPATH' in os.environ: - db_path = os.environ['GALAXY_TEST_DBPATH'] - else: - tempdir = tempfile.mkdtemp() - db_path = os.path.join( tempdir, 'database' ) - file_path = os.path.join( db_path, 'files' ) - try: - os.makedirs( file_path ) - except OSError: - pass - if 'GALAXY_TEST_DBURI' in os.environ: - database_connection = os.environ['GALAXY_TEST_DBURI'] - else: - database_connection = 'sqlite:///' + os.path.join( db_path, 'universe.sqlite' ) - if 'GALAXY_TEST_RUNNERS' in os.environ: - start_job_runners = os.environ['GALAXY_TEST_RUNNERS'] - else: - start_job_runners = None - if 'GALAXY_TEST_DEF_RUNNER' in os.environ: - default_cluster_job_runner = os.environ['GALAXY_TEST_DEF_RUNNER'] - else: - default_cluster_job_runner = 'local:///' - app = UniverseApplication( job_queue_workers = 5, - start_job_runners = start_job_runners, - default_cluster_job_runner = default_cluster_job_runner, - id_secret = 'changethisinproductiontoo', - template_path = "templates", - database_connection = database_connection, - file_path = file_path, - tool_config_file = "tool_conf.xml.sample", - datatype_converters_config_file = "datatype_converters_conf.xml.sample", - tool_path = "tools", - test_conf = "test.conf", - log_destination = "stdout", - use_heartbeat = False, - allow_user_creation = True, - allow_user_deletion = True, - admin_users = 'test(a)bx.psu.edu', - library_import_dir = os.path.join( os.getcwd(), galaxy_test_file_dir ), - user_library_import_dir = os.path.join( os.getcwd(), galaxy_test_file_dir, 'users' ), - global_conf = { "__file__": "universe_wsgi.ini.sample" } ) - - log.info( "Embedded Universe application started" ) - - webapp = buildapp.app_factory( dict(), use_translogger = False, app=app ) - server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) - - atexit.register( teardown ) - t = threading.Thread( target=server.serve_forever ) - t.start() - time.sleep( 2 ) - log.info( "Embedded web server started" ) - - if app: - # TODO: provisions for loading toolbox from file when using external server - test_toolbox.toolbox = app.toolbox - else: - # FIXME: This doesn't work at all now that toolbox requires an 'app' instance - # (to get at datatypes, might just pass a datatype registry directly) - my_app = bunch.Bunch( datatypes_registry = galaxy.datatypes.registry.Registry() ) - test_toolbox.toolbox = tools.ToolBox( 'tool_conf.xml.test', 'tools', my_app ) - - # Test if the server is up - conn = httplib.HTTPConnection( galaxy_test_host, galaxy_test_port ) - conn.request( "GET", "/" ) - assert conn.getresponse().status == 200, "Test HTTP server did not return '200 OK'" - - log.info( "Functional tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_port ) ) - - os.environ['GALAXY_TEST_HOST'] = galaxy_test_host - os.environ['GALAXY_TEST_PORT'] = galaxy_test_port - os.environ['GALAXY_TEST_FILE_DIR'] = galaxy_test_file_dir - -def teardown(): - global server, app - if server: - server.server_close() - server = None - log.info( "Embedded web server stopped" ) - if app: - app.shutdown() - app = None - log.info( "Embedded Universe application stopped" ) - time.sleep(2) - -# def test_toolbox(): -# for test in app.toolbox.get_tests(): -# yield ( test, ) +""" +Functional Tests +"""

1 0

[hg] galaxy 2894: Fix setting the peek when a line is already un...
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ea29f33390d3 changeset: 2894:ea29f33390d3 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Oct 20 10:39:30 2009 -0400 description: Fix setting the peek when a line is already unicode (when does this happen?) 1 file(s) affected in this change: lib/galaxy/datatypes/data.py diffs (15 lines): diff -r 55d479c8d592 -r ea29f33390d3 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Mon Oct 19 12:05:19 2009 -0400 +++ b/lib/galaxy/datatypes/data.py Tue Oct 20 10:39:30 2009 -0400 @@ -136,7 +136,10 @@ line = line.strip() if not line: continue - out.append( '<tr><td>%s</td></tr>' % escape( unicode( line, 'utf-8' ) ) ) + if type( line ) is unicode: + out.append( '<tr><td>%s</td></tr>' % escape( line ) ) + else: + out.append( '<tr><td>%s</td></tr>' % escape( unicode( line, 'utf-8' ) ) ) out.append( '</table>' ) out = "".join( out ) except Exception, exc:

1 0

[hg] galaxy 2895: Show encoded URL, while still allowing unencod...
by Greg Von Kuster 27 Oct '09

27 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/61684a4d6b9e changeset: 2895:61684a4d6b9e user: Kanwei Li <kanwei(a)gmail.com> date: Tue Oct 20 15:34:47 2009 -0400 description: Show encoded URL, while still allowing unencoded ids for backward compatibility. Revert to "display" displaying whole file. 6 file(s) affected in this change: lib/galaxy/web/buildapp.py lib/galaxy/web/controllers/dataset.py lib/galaxy/web/controllers/root.py templates/dataset/large_file.mako templates/root/history_common.mako test/base/twilltestcase.py diffs (213 lines): diff -r ea29f33390d3 -r 61684a4d6b9e lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py Tue Oct 20 10:39:30 2009 -0400 +++ b/lib/galaxy/web/buildapp.py Tue Oct 20 15:34:47 2009 -0400 @@ -77,7 +77,7 @@ webapp.add_route( '/async/:tool_id/:data_id/:data_secret', controller='async', action='index', tool_id=None, data_id=None, data_secret=None ) webapp.add_route( '/:controller/:action', action='index' ) webapp.add_route( '/:action', controller='root', action='index' ) - webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None) + webapp.add_route( '/datasets/:encoded_id/:action/:filename', controller='dataset', action='index', encoded_id=None, filename=None) webapp.add_route( '/u/:username/p/:slug', controller='page', action='display_by_username_and_slug' ) webapp.finalize_config() # Wrap the webapp in some useful middleware diff -r ea29f33390d3 -r 61684a4d6b9e lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Tue Oct 20 10:39:30 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Tue Oct 20 15:34:47 2009 -0400 @@ -199,8 +199,14 @@ return 'This link may not be followed from within Galaxy.' @web.expose - def display(self, trans, dataset_id=None, filename=None, show_all=False, **kwd): + def display(self, trans, encoded_id=None, preview=False, filename=None, to_ext=None, **kwd): """Catches the dataset id and displays file contents as directed""" + + # DEPRECATION: We still support unencoded ids for backward compatibility + try: + dataset_id = int( encoded_id ) + except ValueError: + dataset_id = trans.security.decode_id( encoded_id ) data = trans.app.model.HistoryDatasetAssociation.get( dataset_id ) if not data: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) @@ -208,30 +214,47 @@ if trans.app.security_agent.can_access_dataset( roles, data.dataset ): if data.state == trans.model.Dataset.states.UPLOAD: return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." ) - if filename is None or filename.lower() == "index": - file_path = data.file_name - mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) - trans.response.set_content_type(mime) - trans.log_event( "Display dataset id: %s" % str( dataset_id ) ) - - else: + + if filename and filename != "index": file_path = os.path.join( data.extra_files_path, filename ) - mime, encoding = mimetypes.guess_type( file_path ) - if mime is None: - mime = trans.app.datatypes_registry.get_mimetype_by_extension( ".".split( file_path )[-1] ) - trans.response.set_content_type( mime ) + if os.path.exists( file_path ): + mime, encoding = mimetypes.guess_type( file_path ) + if not mime: + try: + mime = trans.app.datatypes_registry.get_mimetype_by_extension( ".".split( file_path )[-1] ) + except: + mime = "txt" - if os.path.exists( file_path ): - max_peek_size = 1000000 # 1 MB - if show_all or os.stat( file_path ).st_size < max_peek_size: + trans.response.set_content_type( mime ) return open( file_path ) else: + return "Could not find '%s' on the extra files path." % filename + + mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) + trans.response.set_content_type(mime) + trans.log_event( "Display dataset id: %s" % str( dataset_id ) ) + + if to_ext: # Saving the file + trans.response.headers['Content-Length'] = int( os.stat( data.file_name ).st_size ) + if to_ext[0] != ".": + to_ext = "." + to_ext + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = data.name + fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] + trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (data.hid, fname, to_ext) + return open( data.file_name ) + + if os.path.exists( data.file_name ): + max_peek_size = 1000000 # 1 MB + if preview and os.stat( data.file_name ).st_size > max_peek_size: trans.response.set_content_type( "text/html" ) - return trans.fill_template( "/dataset/large_file.mako", - truncated_data = open( file_path ).read(max_peek_size), + return trans.stream_template_mako( "/dataset/large_file.mako", + truncated_data = open( data.file_name ).read(max_peek_size), data = data ) + else: + return open( data.file_name ) else: - raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % ( filename ) ) + raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name ) else: return trans.show_error_message( "You are not allowed to access this dataset" ) diff -r ea29f33390d3 -r 61684a4d6b9e lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Tue Oct 20 10:39:30 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Tue Oct 20 15:34:47 2009 -0400 @@ -139,49 +139,13 @@ @web.expose def display( self, trans, id=None, hid=None, tofile=None, toext=".txt", **kwd ): """ - Returns data directly into the browser. - Sets the mime-type according to the extension + Backward compatibility. """ - if hid is not None: - try: - hid = int( hid ) - except: - return "hid '%s' is invalid" %str( hid ) - history = trans.get_history() - for dataset in history.datasets: - if dataset.hid == hid: - data = dataset - break - else: - raise Exception( "No dataset with hid '%d'" % hid ) + if tofile: + to_ext = toext else: - try: - data = self.app.model.HistoryDatasetAssociation.get( id ) - except: - return "Dataset id '%s' is invalid" %str( id ) - if data: - user, roles = trans.get_user_and_roles() - if trans.app.security_agent.can_access_dataset( roles, data.dataset ): - mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) - trans.response.set_content_type(mime) - if tofile: - fStat = os.stat(data.file_name) - trans.response.headers['Content-Length'] = int(fStat.st_size) - if toext[0:1] != ".": - toext = "." + toext - valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = data.name - fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] - trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (data.hid, fname, toext) - trans.log_event( "Display dataset id: %s" % str(id) ) - try: - return open( data.file_name ) - except: - return "This dataset contains no content" - else: - return "You are not allowed to access this dataset" - else: - return "No dataset with id '%s'" % str( id ) + to_ext = None + return trans.webapp.controllers['dataset'].display( trans, encoded_id=id, to_ext=to_ext ) @web.expose def display_child(self, trans, parent_id=None, designation=None, tofile=None, toext=".txt"): diff -r ea29f33390d3 -r 61684a4d6b9e templates/dataset/large_file.mako --- a/templates/dataset/large_file.mako Tue Oct 20 10:39:30 2009 -0400 +++ b/templates/dataset/large_file.mako Tue Oct 20 15:34:47 2009 -0400 @@ -2,8 +2,8 @@ <div class="warningmessagelarge"> This dataset is large and only the first megabyte is shown below.<br /> - <a href="${h.url_for( controller='dataset', action='display', dataset_id=data.id, show_all=True )}">Show all</a> | - <a href="${h.url_for( controller='root', action='display', id=data.id, tofile='yes', toext=data.ext )}">Save</a> + <a href="${h.url_for( controller='dataset', action='display', encoded_id=trans.security.encode_id( data.id ), filename='' )}">Show all</a> | + <a href="${h.url_for( controller='dataset', action='display', encoded_id=trans.security.encode_id( data.id ), to_ext=data.ext )}">Save</a> </div> <pre> diff -r ea29f33390d3 -r 61684a4d6b9e templates/root/history_common.mako --- a/templates/root/history_common.mako Tue Oct 20 10:39:30 2009 -0400 +++ b/templates/root/history_common.mako Tue Oct 20 15:34:47 2009 -0400 @@ -33,7 +33,7 @@ <img src="${h.url_for('/static/images/pencil_icon_grey.png')}" width='16' height='16' alt='edit attributes' title='edit attributes' class='button edit' border='0'> %endif %else: - <a class="icon-button display" title="display data" href="${h.url_for( controller='dataset', dataset_id=data.id, action='display', filename='index')}" target="galaxy_main"></a> + <a class="icon-button display" title="display data" href="${h.url_for( controller='dataset', action='display', encoded_id=trans.security.encode_id( data.id ), preview=True, filename='' )}" target="galaxy_main"></a> %if user_owns_dataset: <a class="icon-button edit" title="edit attributes" href="${h.url_for( controller='root', action='edit', id=data.id )}" target="galaxy_main"></a> %endif @@ -87,7 +87,7 @@ <div class="info">${_('Info: ')}${data.display_info()}</div> <div> %if data.has_data: - <a href="${h.url_for( controller='root', action='display', id=data.id, tofile='yes', toext=data.ext )}" target="_blank">save</a> + <a href="${h.url_for( controller='dataset', action='display', encoded_id=trans.security.encode_id( data.id ), to_ext=data.ext )}">save</a> %if user_owns_dataset: | <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main">rerun</a> %endif diff -r ea29f33390d3 -r 61684a4d6b9e test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Oct 20 10:39:30 2009 -0400 +++ b/test/base/twilltestcase.py Tue Oct 20 15:34:47 2009 -0400 @@ -419,9 +419,9 @@ self.visit_url( "%s/dataset/undelete?id=%s" % ( self.url, hda_id ) ) if check_str: self.check_page_for_string( check_str ) - def display_history_item( self, id, check_str='' ): + def display_history_item( self, hda_id, check_str='' ): """Displays a history item - simulates eye icon click""" - self.visit_url( '%s/datasets/%s/display/index' % ( self.url, id ) ) + self.visit_url( '%s/datasets/%s/display/' % ( self.url, self.security.encode_id( hda_id ) ) ) if check_str: self.check_page_for_string( check_str ) self.home() @@ -554,7 +554,7 @@ def verify_composite_datatype_file_content( self, file_name, hda_id ): local_name = self.get_filename( file_name ) temp_name = self.get_filename( 'temp_%s' % file_name ) - self.visit_url( "%s/datasets/%s/display/%s" % ( self.url, hda_id, file_name ) ) + self.visit_url( "%s/datasets/%s/display/%s" % ( self.url, self.security.encode_id( hda_id ), file_name ) ) data = self.last_page() file( temp_name, 'wb' ).write( data ) try:

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Re: [galaxy-dev] Error in my functional test
by Vipin TS 26 Oct '09

26 Oct '09

Hi Nate, I tried to run the tool with a small input file. Then that case also the test fails and returns the same error message. FAIL: mGenePredict ( mgenepredict ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/galaxy/galaxy-2.1.2009/test/functional/test_toolbox.py", line 114, in test_tool self.do_it() File "/home/galaxy/galaxy-2.1.2009/test/functional/test_toolbox.py", line 54, in do_it self.verify_dataset_correctness( file ) File "/home/galaxy/galaxy-2.1.2009/test/base/twilltestcase.py", line 323, in verify_dataset_correctness if wait: self.wait() #wait for job to finish File "/home/galaxy/galaxy-2.1.2009/test/base/twilltestcase.py", line 617, in wait self.assertNotEqual(count, maxiter) AssertionError: 20 == 20 Also I can find that the job is not finished even though I got the fail message. I confirmed the same, when I run the test again it produces an error message stating that the Galaxy port is already in use. I hope my assumption is true, if not please let me know. Many thanks, Vipin T S

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Error in my functional test
by Vipin Thankam Sreedharan 23 Oct '09

23 Oct '09

Hi all, I wrote a functional test for my tool. Here is the test code. <tests> <test> <param name="source" value="history" /> <param name="fasta_input" value="tair9_chr4_10000.fas" ftype="fasta" /> <param name="source" value="pretrained" /> <param name="organism" value="arabidopsis" /> <output name="output" file="tair9_chr4_output.gff3" /> </test> </tests> While running the test I am getting an error message like the following. ERROR: test module functional in /home/galaxy/galaxy-2.1.2009/test ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/galaxy/galaxy-2.1.2009/eggs/py2.5-noplatform/nose-0.9.1.dev_r101-py2.5.egg/nose/suite.py", line 46, in run self.setUp() File "/home/galaxy/galaxy-2.1.2009/eggs/py2.5-noplatform/nose-0.9.1.dev_r101-py2.5.egg/nose/suite.py", line 200, in setUp try_run(self.module, names) File "/home/galaxy/galaxy-2.1.2009/eggs/py2.5-noplatform/nose-0.9.1.dev_r101-py2.5.egg/nose/util.py", line 200, in try_run return func() File "/home/galaxy/galaxy-2.1.2009/test/functional/__init__.py", line 88, in setup server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) File "/home/galaxy/galaxy-2.1.2009/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/httpserver.py", line 1257, in serve threadpool_options=threadpool_options) File "/home/galaxy/galaxy-2.1.2009/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/httpserver.py", line 1107, in __init__ RequestHandlerClass, ssl_context) File "/home/galaxy/galaxy-2.1.2009/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/httpserver.py", line 1087, in __init__ RequestHandlerClass, ssl_context) File "/home/galaxy/galaxy-2.1.2009/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/httpserver.py", line 328, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib/python2.5/SocketServer.py", line 330, in __init__ self.server_bind() File "/usr/lib/python2.5/BaseHTTPServer.py", line 101, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib/python2.5/SocketServer.py", line 341, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind error: (98, 'Address already in use') ************************************************************ It will be great if you can give me a suggestion. Thanks in advance, Vipin T S

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